rs3807153
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_020632.3(ATP6V0A4):āc.1739T>Cā(p.Met580Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0592 in 1,613,950 control chromosomes in the GnomAD database, including 3,999 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M580I) has been classified as Uncertain significance.
Frequency
Consequence
NM_020632.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP6V0A4 | NM_020632.3 | c.1739T>C | p.Met580Thr | missense_variant | 17/22 | ENST00000310018.7 | |
ATP6V0A4 | NM_130840.3 | c.1739T>C | p.Met580Thr | missense_variant | 16/21 | ||
ATP6V0A4 | NM_130841.3 | c.1739T>C | p.Met580Thr | missense_variant | 16/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP6V0A4 | ENST00000310018.7 | c.1739T>C | p.Met580Thr | missense_variant | 17/22 | 1 | NM_020632.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0908 AC: 13799AN: 152026Hom.: 992 Cov.: 31
GnomAD3 exomes AF: 0.0658 AC: 16551AN: 251412Hom.: 819 AF XY: 0.0666 AC XY: 9043AN XY: 135866
GnomAD4 exome AF: 0.0559 AC: 81714AN: 1461806Hom.: 2997 Cov.: 41 AF XY: 0.0571 AC XY: 41515AN XY: 727222
GnomAD4 genome ? AF: 0.0910 AC: 13851AN: 152144Hom.: 1002 Cov.: 31 AF XY: 0.0908 AC XY: 6756AN XY: 74382
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Dec 10, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | This variant is associated with the following publications: (PMID: 16611712, 27884173, 10973252, 20981092, 24252324) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Autosomal recessive distal renal tubular acidosis Benign:2
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Aug 25, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. - |
Renal tubular acidosis, distal, 3, with or without sensorineural hearing loss Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 01, 2000 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at